Prostate cancer is the most commonly diagnosed cancer and the second most common cause of death from cancer in American men. Prostate cancer cells often initially rely on androgen (e.g., testosterone) for their growth and maintenance. Therefore, androgen withdrawal, by castration or through the use of an anti-androgenic drug, is a common treatment for prostate cancer. In many cases, however, prostate cancer patients develop androgen-independent prostate cancer so that androgen withdrawal treatment is no longer effective.
The complex process of prostate tumor growth and development involves multiple gene products. Therefore, it is important to identify genes involved in tumor development, growth, and androgen dependence, particularly those genes and gene products that can serve as targets for the diagnosis, prevention, and treatment of prostate cancer.
The present invention is based, at least in part, on the discovery of a cDNA molecule encoding a novel protein called Ubiquitin-Conjugating Enzyme-Like Protein (UBCLP). This protein, fragments, derivatives, and variants thereof are collectively referred to as xe2x80x9cpolypeptides of the inventionxe2x80x9d or xe2x80x9cproteins of the invention.xe2x80x9d Nucleic acid molecules encoding polypeptides of the invention are collectively referred to as xe2x80x9cnucleic acids of the invention.xe2x80x9d
The polypeptides, and nucleic acids of the invention are potential targets for the development of therapeutic compounds. Because androgen is required for growth and survival of androgen-dependent prostate cancer cells, genes such UBCLP whose expression is decreased in the presence of casodex, an anti-androgen, are potential therapeutic targets. An agent which decreases the expression or activity of UBCLP may slow the growth of, arrest the growth of, or kill prostate cancer cells, including androgen-independent prostate cancer cells. An agent which reduces the expression or activity of UBCLP may reduce the growth of androgen-independent prostate cancer or cause an androgen-dependent cancer to become androgen-dependent so that it can be treated with standard androgen withdrawal therapy. Of course, such an agent might also be useful for the treatment of an androgen-dependent prostate cancer.
Useful therapeutic agents can be identified using androgen-dependent prostate cancer cells (e.g., CWR22 cells or LNCaP cells) or androgen-independent prostate cancer cells (e.g., CWR22R cells or L3 LNCaP cells) which express UBCLP. The growth of such cells in the presence and absence of a test agent is measured (in the presence or absence of an androgen). Compounds which reduce cell growth, reduce UBCLP expression, or reduce UBCLP activity are potential therapeutic agents for the treatment of prostate cancer (e.g., androgen-independent prostate cancer).
Because UBCLP expression is decreased in the presence of casodex, an antiandrogen, UBCLP expression or activity can serve as a marker for monitoring prostate cancer therapies. For example, UBCLP should not be expressed at a significant level in the prostate cancer cells of patients undergoing anti-androgen therapy. An increase over time in UBCLP expression or activity in a patient undergoing anti-androgen therpay indicates that the therapy is becoming less effective. Such an increase can also indicate that the prostate cancer is becoming androgen-independent. In this and other assays of UBCLP expression, the nominal level of expression is usually normalized to the level of a non-regulated (e.g., housekeeping) gene such as actin.
Using the above-described methods one can predict whether a selected compound, e.g., an anti-androgenic compound, can be used to treat a prostate cancer. Importantly, this determination can be made on a patient by patient basis. Thus, one can determine whether or not a particular prostate cancer treatment is likely to benefit a particular patient.
In the various methods of the invention, gene expression can be measured at the mRNA or protein level. Alternatively, expression can be measured indirectly by measuring the activity of UBCLP protein.
In another aspect, the present invention provides a method for detecting the presence of UBCLP activity or expression in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of UBCLP activity such that the presence of UBCLP activity is detected in the biological sample.
In another aspect, the invention provides a method for treating prostate cancer by modulating the expression or activity of UBCLP, the method comprising contacting a cell with an agent that modulate""s (inhibits or stimulates, preferably inhibits) UBCLP activity or expression such that UBCLP activity or expression in the cell is modulated. In one embodiment, the agent is an antibody that specifically binds to UBCLP. In another embodiment, the agent modulates expression of UBCLP by modulating transcription, modulating mRNA splicing, or modulating mRNA translation. In yet another embodiment, the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of UBCLP.
In one embodiment, the methods of the present invention are used to treat a subject having a prostate cancer characterized by aberrant UBCLP protein activity or expression (e.g., constitutive expression in absence of an androgen or abnormally high expression in the presence of estrogen) by administering an agent which is a UBCLP modulator to the subject. The modulator can be a peptide, peptidomimetic, or small molecule, e.g., an organic molecule.
The present invention also provides a diagnostic assay for identifying whether a patient has or is at risk of developing prostate cancer by detecting the presence or absence of a genetic lesion or mutation in the UBCLP gene of the invention characterized by at least one of: (i) aberrant modification or mutation of a gene of the invention; (ii) mis-regulation of a gene of the invention (e.g., constitutive expression in the absence of androgen); and (iii) aberrant post-translational modification of a protein encoded by a gene of the invention.
In another aspect, the invention provides a method for identifying a compound for the treatment of prostate cancer (e.g., an androgen-independent prostate cancer or an androgen-dependent prostate cancer) by identifying a compound that binds to or modulates the activity of UBCLP protein. In general, such methods entail measuring a biological activity of UBCLP in the presence and absence of a test compound and identifying those compounds which alter the measured activity of UBCLP.
The invention also features methods for identifying a compound which modulates the expression of UBCLP (at the mRNA or protein level) by measuring the expression of UBCLP nucleic acid or protein of the invention in the presence and absence of a compound.
Differential expression refers to both quantitative, as well as qualitative, differences in the expression pattern of a gene in tumor cells treated with a particular compound (e.g., casodex) and untreated tumor cells. A differentially expressed gene can be a target gene. A target gene is a differentially expressed gene involved in a disorder (e.g., prostate cancer) such that modulation of the level of target gene expression or of target gene product activity can act to prevent and/or ameliorate symptoms of the disorder (e.g., androgen-dependent or androgen-independent prostate cancer). Compounds that modulate the expression of the target gene or the activity of the target gene product can be used in the treatment or prevention of the disorder. Thus, compounds that modulate the expression of a prostate cancer target gene or the activity of the gene product of a prostate cancer target gene can be used in treatments to deter benign cells from developing into prostate cancer cells. Still further, compounds that modulate the expression of a prostate cancer target gene or the activity of the gene product of a prostate cancer target gene can be used to design a preventive intervention in pre-neoplastic cells in individuals at high risk for developing prostate cancer.
An androgen-dependent prostate cancer cell is a cell that requires androgen for continued cell division. Conversely, and androgen-independent prostate cancer cell is a cell that can continue to divide in the absence of androgen.
Other features and advantages of the invention will be apparent from the following detailed description and claims.
The invention features nucleic acid molecules which are at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the nucleotide sequence of SEQ ID NO:1 or 3.
The invention features nucleic acid molecules which include a fragment of at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1200) nucleotides of the nucleotide sequence of SEQ ID NO:1.
The invention also features nucleic acid molecules which include a nucleotide sequence encoding a protein having an amino acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the amino acid sequence of SEQ ID NO:2.
In preferred embodiments, the nucleic acid molecules have the nucleotide sequence of SEQ ID NO:1.
Also within the invention are nucleic acid molecules which encode a fragment of a polypeptide having the amino acid sequence of SEQ ID NO:2, the fragment including at least 15 (25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of SEQ ID NO:2.
The invention includes nucleic acid molecules which encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule having a nucleic acid sequence encoding SEQ ID NO:2 under stringent conditions.
Also within the invention are: isolated polypeptides or proteins having an amino acid sequence that is at least about 65%, preferably 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ ID NO:2.
Also within the invention are: isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 65%, preferably 75%, 85%, or 95% identical to a nucleic acid sequence encoding SEQ ID NO:2; and isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:1 or 3.
Also within the invention are polypeptides which are a naturally occurring allelic variant of a polypeptide that includes the amino acid sequence of SEQ ID NO:2, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule having the sequence of SEQ ID NO: 1 or 3 under stringent conditions.
The invention also features nucleic acid molecules that hybridize tinder stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1or 3. In other embodiments, the nucleic acid molecules are at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides in length and hybridizes tinder stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:1 or 3.
In another embodiment, the invention provides an isolated nucleic acid molecule which is antisense to the coding strand of a nucleic acid of the invention.
Another aspect of the invention provides vectors, e.g., recombinant expression vectors, comprising a nucleic acid molecule of the invention. In another embodiment the invention provides host cells containing such a vector. The invention also provides methods for producing a polypeptide of the invention by culturing, in a suitable medium, a host cell of the invention containing a recombinant expression vector such that a polypeptide of the invention is produced.
Another aspect of this invention features isolated or recombinant proteins and polypeptides of the invention. Preferred proteins and polypeptides possess at least one biological activity possessed by the corresponding naturally-occurring human polypeptide. An activity, a biological activity, and a functional activity of a polypeptide of the invention refers to an activity exerted by a protein, polypeptide or nucleic acid molecule of the invention on a responsive cell as determined in vivo, or in vitro, according to standard techniques. Such activities can be a direct activity, such as an association with or an enzymatic activity on a second protein or an indirect activity, such as a cellular signaling activity mediated by interaction of the protein with a second protein.
In one embodiment, a polypeptide of the invention has an amino acid sequence sufficiently identical to an identified domain of a polypeptide of the invention. As used herein, the term xe2x80x9csufficiently identicalxe2x80x9d refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity. For example, amino acid or nucleotide sequences which contain a common structural domain having about 65% identity, preferably 75% identity, more preferably 85%, 95%, or 98% identity are defined herein as sufficiently identical.
In one embodiment, the isolated polypeptide and lacks both a transmembrane and a cytoplasmic domain. In another embodiment the polypeptide lacks both a transmembrane domain and a cytoplasmic domain and is soluble under physiological conditions.
The polypeptides of the present invention, or biologically active portions thereof, can be operably linked to a heterologous amino acid sequence to form a fusion protein. The invention further features antibodies that specifically bind a polypeptide of the invention such as monoclonal or polyclonal antibodies. In addition, the polypeptides of the invention or biologically active portions thereof can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
In another aspect, the present invention provides methods for detecting the presence of the activity or expression of a polypeptide of the invention in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of activity such that the presence of activity is detected in the biological sample.
Other features and advantages of the invention will be apparent from the following detailed description and claims.